#!/usr/bin/env python3
"""Module containing the Pdbselchain class and the command line interface."""
from typing import Optional
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
[docs]
class Pdbselchain(BiobbObject):
"""
| biobb_pdb_tools Pdbselchain
| Extracts one or more chains from a PDB file.
| This tool extracts a specific chain or list of chains from a PDB file, discarding all others.
Args:
input_file_path (str): Input PDB file. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/data/pdb_tools/input_pdb_selchain.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_file_path (str): PDB file with selected chains. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/reference/pdb_tools/ref_pdb_selchain.pdb>`_. Accepted formats: pdb (edam:format_1476).
properties (dic):
* **chains** (*str*) - ('A') Chain or list of chains (comma separated) to extract from the PDB file.
* **binary_path** (*str*) - ("pdb_selchain") Path to the pdb_selchain executable binary.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
Examples:
This is a use example of how to use the building block from Python::
from biobb_pdb_tools.pdb_tools.biobb_pdb_selchain import biobb_pdb_selchain
prop = {
'chains': 'A,B'
}
biobb_pdb_selchain(input_file_path='/path/to/input.pdb',
output_file_path='/path/to/output.pdb',
properties=prop)
Info:
* wrapped_software:
* name: pdb_tools
* version: >=2.5.0
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(
self, input_file_path, output_file_path, properties=None, **kwargs
) -> None:
properties = properties or {}
super().__init__(properties)
self.locals_var_dict = locals().copy()
self.io_dict = {
"in": {"input_file_path": input_file_path},
"out": {"output_file_path": output_file_path},
}
self.binary_path = properties.get("binary_path", "pdb_selchain")
self.chains = properties.get("chains", "A")
self.properties = properties
self.check_init(properties)
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`Pdbselchain <biobb_pdb_tools.pdb_tools.pdb_selchain>` object."""
if self.check_restart():
return 0
self.stage_files()
instructions = []
if self.chains:
instructions.append("-" + str(self.chains))
fu.log("Appending chains to select", self.out_log, self.global_log)
self.cmd = [
self.binary_path,
" ".join(instructions),
self.stage_io_dict["in"]["input_file_path"],
">",
self.io_dict["out"]["output_file_path"],
]
fu.log(" ".join(self.cmd), self.out_log, self.global_log)
fu.log(
"Creating command line with instructions and required arguments",
self.out_log,
self.global_log,
)
self.run_biobb()
self.copy_to_host()
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
def biobb_pdb_selchain(
input_file_path: str,
output_file_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create :class:`Pdbselchain <biobb_pdb_tools.pdb_tools.pdb_selchain>` class and
execute the :meth:`launch() <biobb_pdb_tools.pdb_tools.pdb_selchain.launch>` method."""
return Pdbselchain(**dict(locals())).launch()
biobb_pdb_selchain.__doc__ = Pdbselchain.__doc__
main = Pdbselchain.get_main(biobb_pdb_selchain, "Extracts one or more chains from a PDB file.")
if __name__ == "__main__":
main()